View source: R/VDJ_Vgene_usage_barplot.R
VDJ_Vgene_usage_barplot | R Documentation |
Produces a barplot with the most frequently used IgH and IgK/L Vgenes.
VDJ_Vgene_usage_barplot( VDJ, group.by, HC.gene.number, LC.Vgene, LC.gene.number, platypus.version, is.bulk )
VDJ |
Either (for platypus version "v2") output from VDJ_analyze function. This should be a list of clonotype dataframes, with each list element corresponding to a single VDJ repertoire, OR (for platypus version "v3") the the VDJ matrix output of the VDJ_GEX_matrix() function (VDJ.GEX.matrix.output[[1]]) |
group.by |
Character. Defaults to "sample_id". Column name of VDJ to group plot by. |
HC.gene.number |
Numeric value indicating the top genes to be dispayed. If this number is higher than the total number of unique HC V genes in the VDJ repertoire, then this number is equal to the number of unique HC V genes. |
LC.Vgene |
Logical indicating whether to make a barplot of the LC V genes distribution. Default is set to FALSE. |
LC.gene.number |
Numeric value indicating the top genes to be dispayed. If this number is higher than the total number of unique LC V genes in the VDJ repertoire, then this number is equal to the number of unique LC V genes. |
platypus.version |
Character. Defaults to "v3". Can be "v2" or "v3" dependent on the input format |
is.bulk |
logical value indicating whether the VDJ input was generated from bulk-sequencing data using the bulk_to_vgm function. If is.bulk = T, the VDJ_Vgene_usage_barplot function is compatible for use with bulk data. Defaults to False (F). |
Returns a list of ggplot objects which show the distribution of IgH and IgK/L V genes for the most used V genes.
## Not run: VDJ_Vgene_usage_barplot(VDJ = Platypus::small_vgm[[1]], HC.gene.number = 2, platypus.version = "v3") ## End(Not run)
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